183 lines
8.3 KiB
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183 lines
8.3 KiB
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>prd command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>prd steps t_event n_dephase t_dephase t_corr compute-ID seed keyword value ...
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</PRE>
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<UL><LI>steps = total # of timesteps to run (not including dephasing/quenching)
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<LI>t_event = timestep interval between event checks
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<LI>n_dephase = number of velocity randomizations to perform in each dephase run
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<LI>t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase
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<LI>t_corr = number of timesteps within which 2 consecutive events are considered to be correlated
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<LI>compute-id = ID of the compute used for event detection
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<LI>random_seed = random # seed (positive integer)
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>min</I> or <I>temp</I> or <I>vel</I>
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<PRE> <I>min</I> values = etol ftol maxiter maxeval
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etol = stopping tolerance for energy, used in quenching
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ftol = stopping tolerance for force, used in quenching
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maxiter = max iterations of minimize, used in quenching
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maxeval = max number of force/energy evaluations, used in quenching
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<I>temp</I> value = Tdephase
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Tdephase = target temperature for velocity randomization, used in dephasing
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<I>vel</I> values = loop dist
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loop = <I>all</I> or <I>local</I> or <I>geom</I>, used in dephasing
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dist = <I>uniform</I> or <I>gaussian</I>, used in dephasing
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>prd 5000 100 10 10 100 1 54982
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prd 5000 100 10 10 100 1 54982 maxiter 100
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Run Parallel Replica Dynamics (PRD) as described in <A HREF = "#Voter">(Voter)</A>.
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PRD is a method for accelerated dynamics that is suitable for
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infrequent-event systems that obey first-order kinetics. To quote
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from the paper: "The dynamical evolution is characterized by
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vibrational excursions within a potential basin, punctuated by
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occasional transitions between basins." The transition probability is
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characterized by p(t) = k*exp(-kt) where k is the rate constant.
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</P>
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<P>PRD is performed by replicating a system in a particular state on M
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processor partitions. Dephasing is performed with <I>n_dephase</I>
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velocity randomizations each followed by <I>t_dephase</I> MD timesteps to
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eliminate correlations between replicas. If the <I>temp</I> keyword is not
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specified, the target temperature for velocity randomization on each
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replica is the temperature at the timestep replication occured,
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otherwise, it is the temperature specified. Velocity randomization is
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controlled using keywords similar to the <A HREF = "velocity.html">velocity</A>
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command. Following dephasing, independent dynamics runs are performed
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on each partition with periodic stops to check for transition events.
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The number of timesteps between each event check is given by the
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<I>t_event</I> parameter.
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</P>
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<P>Event detection is performed by quenching each replica to make a
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comparison to the previous event. The minimum for detection of
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the first event in each PRD run is obtained from quenching the
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initial configuration. The decision as to whether or not a
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transition event has occurred is determined by the compute with id
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equal to <I>compute_id</I>. For example, the
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<A HREF = "compute_event_displace.html">event/displace</A> compute will detect when
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a given particle in the group has moved greater than a threshold
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distance, signalling that an event has occurred.
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</P>
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<P>The algorithm used for quenching is determined by the
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<A HREF = "min_style.html">min_style</A> command. Parameters for minimization are
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specified with keywords analogous to the <A HREF = "minimize.html">minimize</A>
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command. If a transition event is detected, all replicas are stopped,
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and the simulation clock is advanced by the time accumulated on all
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replica partitions. The clock time between events will be drawn from
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p(t). The simulation on the replica where the transition occurred is
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continued for <I>t_corr</I> timesteps to detect any correlated event
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transitions. The final state from this continued run is replicated on
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all partitions to start the whole process again with a new dephasing
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run.
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</P>
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<P>Each replica within PRD can be simulated on 1 or multiple processors.
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The processor partitions are controlled using the -partition
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command-line switch (see <A HREF = "Section_start.html#2_6">this section</A>). By
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default, the timestep, clock, event number, correlation flag, and
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replica number are written to the screen/log at each event. The clock
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value is the total number of timesteps accumulated on all replicas.
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This value will not necessarily be a multiple of the current timestep
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because the checks for correlated events occur on only 1 replica
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(During a correlated event check, the clock advance will be equal to
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the number of timesteps; otherwise, the clock advance will be equal
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to the number of timesteps multiplied by the number of replicas.) The
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correlation flag will be 1 when an event occurs within <I>t_corr</I>
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timesteps from the previous event and 0 otherwise. The replica is the
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replica number where the event occurred. When restarting a PRD run,
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information from the last event that occurred will be written to the
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screen. The PRD run will terminate when the total number of timesteps
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(not including timesteps used for quenching or dephasing) is equal to
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<I>steps</I>.
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</P>
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<P>The <A HREF = "thermo.html">thermo</A> for the dephasing, quenching, and dynamics
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can be output to the log files specific to each partition. You will
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notice that following dephasing and quenching, the timestep is reset
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back its' value to continue dynamics at the correct timestep. Timing
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information for the PRD run will be output to the screen/log files
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for each replica. <A HREF = "dump.html">Dump files</A> will only be written at
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timesteps corresponding to an event (during PRD, the dump frequency
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will be ignored). The coordinates within a dump will correspond to
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the new minimum obtained from quenching following a transition. The
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timesteps written into the dump files correspond to the timestep
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at which each event occurred and not the clock. A dump snapshot
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corresponding to the initial minimum used for event detection is
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written at the beginning of each PRD run.
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</P>
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<P>If a restart file is specified, a single restart file will be
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written for a PRD run to allow the run to be continued from the
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last event. It is important to note that restart files will
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only be generated following correlated event detection after
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each event. Therefore, the timestep of a restart file will
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be equal to the timestep of the event plus <I>t_corr</I> if no
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correlated event is detected and a larger timestep if
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correlated events are found. If a PRD run ends without
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detecting an event, no restart file will be written.
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During PRD, the restart interval is taken to be the
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number of events between each write, and not the number of
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timesteps. This interval does not consider correlated
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events. Restart files can use a different number of
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processors or partitions, however, it is assumed that
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<I>t_corr</I> is not changed when restarting a previous run.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>steps</I> and <I>t_corr</I> settings must be integer multiples of
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<I>t_event</I>.
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</P>
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<P>Runs restarted from restart file written during a PRD run will not
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produce identical results due to changes in the random numbers used
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for dephasing.
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</P>
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<P>This command cannot be used when any fixes are defined that keep track
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of elapsed time to perform time-dependent operations. Examples
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include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
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ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
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dt/reset</A> and <A HREF = "fix_deposity.html">fix deposit</A>.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
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<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
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<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
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<A HREF = "velocity.html">velocity</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are <I>min</I> = 40 50 0.1 0.1, no <I>temp</I> setting, and
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<I>vel</I> = <I>geom</I> <I>gaussian</I>.
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</P>
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<HR>
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<A NAME = "Voter"></A>
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<P><B>(Voter)</B> Voter, Montalenti, Germann, Annual Review of Materials
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Research 32, 321 (2002).
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</P>
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</HTML>
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